Loss of DNASE1L3 Drives MDSCs-Mediated Immune Suppression in HCC via HDAC9-Dependent Chromatin Remodeling and CXCL16–CXCR6 Signaling

Abstract Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide, characterized by profound immune dysregulation wherein myeloid-derived suppressor cells (MDSCs) contribute significantly to the immunosuppressive tumor microenvironment (TME) by promoting immune evasion and tumor progression through mechanisms like T-cell suppression and chemokine axis activation; however, the upstream regulatory mechanisms for MDSCs activation remain poorly defined. Deoxyribonuclease 1-like 3 (DNASE1L3), an immunoregulatory nuclease downregulated in multiple cancers, has an unexplored role in modulating MDSCs in HCC. Here, we demonstrate that DNASE1L3 expression is markedly reduced in tumor-infiltrating MDSCs in HCC and that low DNASE1L3 expression correlates with poor patient prognosis. Using Dnase1l3-knockout (KO) mice, we show that DNASE1L3 deficiency leads to accelerated tumor growth, increased MDSC accumulation, and impaired CD8⁺ T cell infiltration. DNASE1L3-deficient MDSCs acquire enhanced immunosuppressive capacity upon exposure to tumor-derived environmental cues. Mechanistically, DNASE1L3 interacts with histone deacetylase 9 (HDAC9) to maintain nuclear transcriptional homeostasis in MDSCs. Loss of DNASE1L3 results in chromatin remodeling and activation of the CXCL16–CXCR6–AKT–NF-κB axis, thereby enhancing MDSC chemotaxis and immunosuppressive function. These findings identify DNASE1L3 as a nuclear immune checkpoint that modulates MDSC behavior through epigenetic and chemokine-mediated pathways. Targeting the DNASE1L3–HDAC9–CXCR6 signaling cascade may offer a novel strategy to reverse immune evasion and restore antitumor immunity in HCC.